BN1839 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 5.9696e-07 1.5297e-05
Layer 2 7.8829e-07 2.7991e-04
Layer 3 2.7585e-06 2.5262e-05
Layer 6 3.7568e-05 3.5768e-03
Layer 5 4.9324e-05 3.3711e-04
Layer 1 1.5733e-01 3.3244e-01
WM 9.9899e-01 6.5773e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
ATP1A1 Expression Distribution
Gene Specificity Score (GSS)
ATP1A1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
ATP1A1 Layer 3 3.1562 0.8797
CALY Layer 3 3.0859 0.8695
C9orf16 Layer 3 3.0117 0.8660
ATP6V1B2 Layer 3 2.8906 0.8629
GNG3 Layer 3 3.1465 0.8606
ATP1A3 Layer 3 3.0195 0.8588
PRDX2 Layer 3 2.9805 0.8585
UQCR10 Layer 4 2.7910 0.8584
ATP2B2 Layer 3 3.1328 0.8583
PGK1 Layer 4 2.9668 0.8583
YPEL3 Layer 4 3.0527 0.8570
PIN1 Layer 3 3.0254 0.8565
CABP1 Layer 3 3.0996 0.8562
CHGA Layer 4 3.2930 0.8562
FAIM2 Layer 4 3.0723 0.8561
NDUFB4 Layer 4 2.7656 0.8559
SLC25A3 Layer 4 2.8711 0.8553
ATP5IF1 Layer 3 2.7939 0.8552
ATP5F1A Layer 3 2.8027 0.8546
WBP2 Layer 3 2.9863 0.8545
GABARAPL2 Layer 4 2.7969 0.8539
PRDX5 Layer 4 3.0117 0.8531
SERPINI1 Layer 4 2.9922 0.8528
FXYD7 Layer 4 3.0059 0.8523
NPTN Layer 2 2.8906 0.8521
MDH1 Layer 3 2.9668 0.8518
NDRG4 Layer 4 2.8652 0.8516
MEF2C Layer 4 3.0957 0.8514
PPA1 Layer 4 2.6836 0.8513
DCTN1 Layer 3 2.8965 0.8512
ATP5F1D Layer 3 2.7422 0.8506
CAPNS1 Layer 3 2.8115 0.8505
SV2A Layer 4 3.0723 0.8504
GRINA Layer 4 3.0000 0.8493
NISCH Layer 3 2.6514 0.8486
SCN1B Layer 3 3.7402 0.8486
TUBB Layer 4 2.8994 0.8485
SCAMP5 Layer 3 2.7363 0.8485
TUBB2A Layer 5 3.0781 0.8482
ATP5MPL Layer 4 2.8770 0.8481
DYNLRB1 Layer 4 2.9570 0.8480
RASD1 Layer 3 2.7422 0.8479
PHYHIP Layer 2 2.9863 0.8478
MAPK10 Layer 4 3.1191 0.8478
BEX4 Layer 4 2.8457 0.8474
ISCU Layer 4 2.9434 0.8470
TAGLN3 Layer 3 3.0586 0.8463
AP2M1 Layer 3 2.9082 0.8463
GRIN1 Layer 3 3.0352 0.8462
MGST3 Layer 4 2.9668 0.8459

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1839
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1839_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1839/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1839/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1839/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1839/report/PD/BN1839_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1839/report/PD/BN1839_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 08:20:31
  • Number of Processes: 10
  • Spending Time: 0h 3m